Starting phenix.real_space_refine on Tue Feb 11 14:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8n_21575/02_2025/6w8n_21575.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8n_21575/02_2025/6w8n_21575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w8n_21575/02_2025/6w8n_21575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8n_21575/02_2025/6w8n_21575.map" model { file = "/net/cci-nas-00/data/ceres_data/6w8n_21575/02_2025/6w8n_21575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8n_21575/02_2025/6w8n_21575.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4084 2.51 5 N 990 2.21 5 O 1046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6160 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3087 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3073 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 4.39, per 1000 atoms: 0.71 Number of scatterers: 6160 At special positions: 0 Unit cell: (94.875, 96.525, 78.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1046 8.00 N 990 7.00 C 4084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 911.0 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.803A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 66 through 99 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.990A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.743A pdb=" N SER A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 205 removed outlier: 5.056A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.766A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.621A pdb=" N VAL A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.070A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 306 through 334 removed outlier: 3.681A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 363 removed outlier: 3.626A pdb=" N GLY A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 373 through 396 removed outlier: 3.574A pdb=" N ARG A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.818A pdb=" N TRP A 410 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.973A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.025A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.803A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 66 through 99 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.628A pdb=" N ALA B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 162 removed outlier: 3.995A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 5.072A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.783A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.614A pdb=" N VAL B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.062A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 306 through 334 removed outlier: 3.685A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 363 removed outlier: 3.633A pdb=" N GLY B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.156A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.812A pdb=" N TRP B 410 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 435 removed outlier: 4.976A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 445 through 470 Proline residue: B 456 - end of helix removed outlier: 4.927A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1877 1.34 - 1.46: 1221 1.46 - 1.57: 3144 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6304 Sorted by residual: bond pdb=" CB VAL B 147 " pdb=" CG1 VAL B 147 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB VAL A 147 " pdb=" CG1 VAL A 147 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.96e+00 bond pdb=" CB VAL B 268 " pdb=" CG2 VAL B 268 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" CA ILE A 388 " pdb=" C ILE A 388 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.46e-02 4.69e+03 1.74e+00 bond pdb=" CB VAL A 268 " pdb=" CG2 VAL A 268 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 ... (remaining 6299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 8342 1.90 - 3.80: 213 3.80 - 5.71: 39 5.71 - 7.61: 5 7.61 - 9.51: 4 Bond angle restraints: 8603 Sorted by residual: angle pdb=" N SER A 444 " pdb=" CA SER A 444 " pdb=" C SER A 444 " ideal model delta sigma weight residual 112.72 107.66 5.06 1.14e+00 7.69e-01 1.97e+01 angle pdb=" C LEU B 195 " pdb=" N CYS B 196 " pdb=" CA CYS B 196 " ideal model delta sigma weight residual 122.54 117.33 5.21 1.65e+00 3.67e-01 9.98e+00 angle pdb=" C LEU A 195 " pdb=" N CYS A 196 " pdb=" CA CYS A 196 " ideal model delta sigma weight residual 122.54 117.35 5.19 1.65e+00 3.67e-01 9.90e+00 angle pdb=" N LEU B 355 " pdb=" CA LEU B 355 " pdb=" C LEU B 355 " ideal model delta sigma weight residual 113.25 117.24 -3.99 1.30e+00 5.92e-01 9.43e+00 angle pdb=" N LEU A 355 " pdb=" CA LEU A 355 " pdb=" C LEU A 355 " ideal model delta sigma weight residual 113.25 117.22 -3.97 1.30e+00 5.92e-01 9.33e+00 ... (remaining 8598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3208 17.75 - 35.50: 372 35.50 - 53.25: 96 53.25 - 70.99: 21 70.99 - 88.74: 5 Dihedral angle restraints: 3702 sinusoidal: 1350 harmonic: 2352 Sorted by residual: dihedral pdb=" CB CYS A 144 " pdb=" SG CYS A 144 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -155.42 69.42 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual -86.00 -155.27 69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CA GLN B 171 " pdb=" C GLN B 171 " pdb=" N ILE B 172 " pdb=" CA ILE B 172 " ideal model delta harmonic sigma weight residual 180.00 -146.04 -33.96 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 3699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 668 0.038 - 0.076: 297 0.076 - 0.114: 86 0.114 - 0.152: 13 0.152 - 0.190: 11 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB THR A 58 " pdb=" CA THR A 58 " pdb=" OG1 THR A 58 " pdb=" CG2 THR A 58 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CB THR B 58 " pdb=" CA THR B 58 " pdb=" OG1 THR B 58 " pdb=" CG2 THR B 58 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB VAL B 101 " pdb=" CA VAL B 101 " pdb=" CG1 VAL B 101 " pdb=" CG2 VAL B 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1072 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 307 " 0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 308 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 298 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C SER A 298 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 307 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO B 308 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.022 5.00e-02 4.00e+02 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1489 2.78 - 3.31: 6153 3.31 - 3.84: 10410 3.84 - 4.37: 12021 4.37 - 4.90: 20530 Nonbonded interactions: 50603 Sorted by model distance: nonbonded pdb=" O GLN A 171 " pdb=" OG SER A 175 " model vdw 2.244 3.040 nonbonded pdb=" O SER B 444 " pdb=" OG SER B 444 " model vdw 2.257 3.040 nonbonded pdb=" O THR A 306 " pdb=" OG1 THR A 306 " model vdw 2.321 3.040 nonbonded pdb=" O THR B 306 " pdb=" OG1 THR B 306 " model vdw 2.327 3.040 nonbonded pdb=" ND2 ASN A 284 " pdb=" OG1 THR A 306 " model vdw 2.338 3.120 ... (remaining 50598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 398 or (resid 3 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 400 through \ 471)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.210 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6304 Z= 0.435 Angle : 0.773 9.512 8603 Z= 0.422 Chirality : 0.048 0.190 1075 Planarity : 0.005 0.041 1044 Dihedral : 16.693 88.743 2160 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 8.14 % Allowed : 21.42 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.27), residues: 788 helix: -1.31 (0.19), residues: 604 sheet: None (None), residues: 0 loop : -3.02 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.006 0.001 HIS A 328 PHE 0.015 0.002 PHE A 459 TYR 0.016 0.002 TYR A 359 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 0.625 Fit side-chains REVERT: A 101 VAL cc_start: 0.8280 (p) cc_final: 0.8042 (p) REVERT: A 104 LYS cc_start: 0.8459 (mptm) cc_final: 0.8173 (mppt) REVERT: A 336 LYS cc_start: 0.8548 (tttp) cc_final: 0.8263 (tttm) REVERT: A 341 MET cc_start: 0.8079 (mtt) cc_final: 0.7845 (mtt) REVERT: A 390 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: A 448 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.5874 (t80) REVERT: B 104 LYS cc_start: 0.8545 (mptm) cc_final: 0.8218 (mppt) REVERT: B 280 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8317 (mt) REVERT: B 336 LYS cc_start: 0.8578 (tttp) cc_final: 0.8294 (tttm) REVERT: B 341 MET cc_start: 0.8074 (mtt) cc_final: 0.7841 (mtt) outliers start: 54 outliers final: 41 residues processed: 151 average time/residue: 0.1649 time to fit residues: 33.3782 Evaluate side-chains 126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 191 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 191 GLN B 284 ASN B 328 HIS B 390 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120287 restraints weight = 7267.660| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.95 r_work: 0.3143 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6304 Z= 0.187 Angle : 0.655 10.281 8603 Z= 0.322 Chirality : 0.043 0.192 1075 Planarity : 0.004 0.043 1044 Dihedral : 10.982 89.326 923 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.03 % Allowed : 25.94 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.29), residues: 788 helix: -0.20 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -2.56 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 324 HIS 0.003 0.001 HIS B 327 PHE 0.018 0.001 PHE A 459 TYR 0.017 0.002 TYR B 313 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.653 Fit side-chains REVERT: A 101 VAL cc_start: 0.8312 (p) cc_final: 0.8055 (p) REVERT: A 104 LYS cc_start: 0.8479 (mptm) cc_final: 0.8083 (mptt) REVERT: A 280 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8261 (mt) REVERT: A 336 LYS cc_start: 0.8557 (tttp) cc_final: 0.8327 (tttm) REVERT: A 394 TRP cc_start: 0.8940 (OUTLIER) cc_final: 0.8493 (t-100) REVERT: A 448 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.5735 (t80) REVERT: A 460 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5792 (tt) REVERT: B 104 LYS cc_start: 0.8486 (mptm) cc_final: 0.8097 (mptt) REVERT: B 335 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7933 (ptp-170) REVERT: B 336 LYS cc_start: 0.8598 (tttp) cc_final: 0.8336 (tttm) REVERT: B 394 TRP cc_start: 0.8956 (OUTLIER) cc_final: 0.8498 (t-100) outliers start: 40 outliers final: 20 residues processed: 121 average time/residue: 0.1607 time to fit residues: 26.2644 Evaluate side-chains 106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119867 restraints weight = 7384.887| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.97 r_work: 0.3118 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6304 Z= 0.223 Angle : 0.625 9.437 8603 Z= 0.308 Chirality : 0.042 0.223 1075 Planarity : 0.004 0.041 1044 Dihedral : 8.943 63.270 883 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.79 % Allowed : 26.85 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.29), residues: 788 helix: 0.24 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -2.29 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS A 166 PHE 0.014 0.001 PHE A 459 TYR 0.013 0.002 TYR A 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 0.646 Fit side-chains REVERT: A 101 VAL cc_start: 0.8286 (p) cc_final: 0.8038 (p) REVERT: A 104 LYS cc_start: 0.8356 (mptm) cc_final: 0.7942 (mptt) REVERT: A 147 VAL cc_start: 0.8282 (p) cc_final: 0.8050 (t) REVERT: A 280 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 336 LYS cc_start: 0.8527 (tttp) cc_final: 0.8294 (tttm) REVERT: A 394 TRP cc_start: 0.8912 (OUTLIER) cc_final: 0.8451 (t-100) REVERT: A 448 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.5787 (t80) REVERT: A 460 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5876 (tt) REVERT: B 104 LYS cc_start: 0.8349 (mptm) cc_final: 0.7958 (mptt) REVERT: B 335 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7973 (ptp-170) REVERT: B 336 LYS cc_start: 0.8565 (tttp) cc_final: 0.8283 (tttm) REVERT: B 394 TRP cc_start: 0.8922 (OUTLIER) cc_final: 0.8429 (t-100) REVERT: B 448 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.5972 (t80) outliers start: 45 outliers final: 25 residues processed: 125 average time/residue: 0.1682 time to fit residues: 28.6808 Evaluate side-chains 112 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 77 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121625 restraints weight = 7410.770| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.97 r_work: 0.3149 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6304 Z= 0.194 Angle : 0.604 9.337 8603 Z= 0.296 Chirality : 0.041 0.246 1075 Planarity : 0.004 0.040 1044 Dihedral : 8.451 59.779 880 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 7.24 % Allowed : 25.94 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 788 helix: 0.62 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.09 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.004 0.001 HIS A 166 PHE 0.013 0.001 PHE A 459 TYR 0.014 0.002 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 81 time to evaluate : 0.586 Fit side-chains REVERT: A 101 VAL cc_start: 0.8264 (p) cc_final: 0.8022 (p) REVERT: A 104 LYS cc_start: 0.8331 (mptm) cc_final: 0.7941 (mptt) REVERT: A 280 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8208 (mt) REVERT: A 394 TRP cc_start: 0.8903 (OUTLIER) cc_final: 0.8431 (t-100) REVERT: A 448 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.5918 (t80) REVERT: A 460 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5863 (tt) REVERT: B 104 LYS cc_start: 0.8326 (mptm) cc_final: 0.7959 (mptt) REVERT: B 311 LEU cc_start: 0.8489 (mt) cc_final: 0.8216 (mm) REVERT: B 335 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7822 (ptp-170) REVERT: B 336 LYS cc_start: 0.8554 (tttp) cc_final: 0.8274 (tttm) REVERT: B 394 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8425 (t-100) REVERT: B 448 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.5956 (t80) outliers start: 48 outliers final: 27 residues processed: 124 average time/residue: 0.1569 time to fit residues: 26.5989 Evaluate side-chains 109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129889 restraints weight = 7171.073| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.88 r_work: 0.3173 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6304 Z= 0.190 Angle : 0.587 9.166 8603 Z= 0.290 Chirality : 0.041 0.200 1075 Planarity : 0.004 0.039 1044 Dihedral : 7.737 59.983 873 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.94 % Allowed : 25.94 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 788 helix: 0.82 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.26 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.011 0.001 PHE A 459 TYR 0.013 0.002 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 75 time to evaluate : 0.723 Fit side-chains REVERT: A 101 VAL cc_start: 0.8221 (p) cc_final: 0.7981 (p) REVERT: A 104 LYS cc_start: 0.8280 (mptm) cc_final: 0.7887 (mptt) REVERT: A 280 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8155 (mt) REVERT: A 394 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8395 (t-100) REVERT: A 448 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.5982 (t80) REVERT: A 460 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5855 (tt) REVERT: B 104 LYS cc_start: 0.8274 (mptm) cc_final: 0.7900 (mptt) REVERT: B 311 LEU cc_start: 0.8456 (mt) cc_final: 0.8167 (mm) REVERT: B 335 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7837 (ptp-170) REVERT: B 336 LYS cc_start: 0.8521 (tttp) cc_final: 0.8205 (tttm) REVERT: B 394 TRP cc_start: 0.8911 (OUTLIER) cc_final: 0.8400 (t-100) REVERT: B 448 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.5320 (t80) REVERT: B 451 MET cc_start: 0.6919 (tmm) cc_final: 0.6582 (tmm) REVERT: B 452 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6578 (mp10) outliers start: 46 outliers final: 28 residues processed: 115 average time/residue: 0.1691 time to fit residues: 26.5708 Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122775 restraints weight = 7233.226| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.93 r_work: 0.3134 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6304 Z= 0.231 Angle : 0.612 9.150 8603 Z= 0.301 Chirality : 0.041 0.225 1075 Planarity : 0.004 0.038 1044 Dihedral : 7.703 59.137 871 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.69 % Allowed : 25.94 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 788 helix: 0.88 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.24 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.027 0.001 PHE B 459 TYR 0.014 0.002 TYR B 359 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 73 time to evaluate : 0.683 Fit side-chains REVERT: A 101 VAL cc_start: 0.8231 (p) cc_final: 0.7990 (p) REVERT: A 104 LYS cc_start: 0.8297 (mptm) cc_final: 0.7905 (mptt) REVERT: A 280 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8201 (mt) REVERT: A 394 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.8406 (t-100) REVERT: A 448 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6049 (t80) REVERT: A 460 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5838 (tt) REVERT: B 51 MET cc_start: 0.9130 (mmt) cc_final: 0.8530 (mmt) REVERT: B 104 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7900 (mptt) REVERT: B 335 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7948 (ptp-170) REVERT: B 336 LYS cc_start: 0.8532 (tttp) cc_final: 0.8220 (tttm) REVERT: B 394 TRP cc_start: 0.8936 (OUTLIER) cc_final: 0.8422 (t-100) REVERT: B 448 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.5330 (t80) REVERT: B 451 MET cc_start: 0.6924 (tmm) cc_final: 0.6581 (tmm) REVERT: B 452 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6579 (mp10) outliers start: 51 outliers final: 30 residues processed: 120 average time/residue: 0.1500 time to fit residues: 24.7965 Evaluate side-chains 112 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 chunk 25 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122115 restraints weight = 7300.502| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.98 r_work: 0.3196 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6304 Z= 0.155 Angle : 0.589 9.062 8603 Z= 0.285 Chirality : 0.040 0.234 1075 Planarity : 0.004 0.038 1044 Dihedral : 7.272 59.827 869 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.79 % Allowed : 27.30 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.31), residues: 788 helix: 1.07 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.25 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 324 HIS 0.004 0.001 HIS A 327 PHE 0.020 0.001 PHE B 459 TYR 0.014 0.001 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 83 time to evaluate : 0.646 Fit side-chains REVERT: A 104 LYS cc_start: 0.8285 (mptm) cc_final: 0.7913 (mptt) REVERT: A 214 MET cc_start: 0.7618 (mtp) cc_final: 0.7389 (mtp) REVERT: A 359 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.6967 (t80) REVERT: A 394 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.8420 (t-100) REVERT: A 448 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6147 (t80) REVERT: B 51 MET cc_start: 0.9101 (mmt) cc_final: 0.8535 (mmt) REVERT: B 104 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7892 (mptt) REVERT: B 335 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7779 (ptp-170) REVERT: B 336 LYS cc_start: 0.8501 (tttp) cc_final: 0.8221 (tttm) REVERT: B 359 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 394 TRP cc_start: 0.8938 (OUTLIER) cc_final: 0.8402 (t-100) REVERT: B 448 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.5858 (t80) REVERT: B 451 MET cc_start: 0.6970 (tmm) cc_final: 0.6690 (tmm) outliers start: 45 outliers final: 27 residues processed: 119 average time/residue: 0.1612 time to fit residues: 26.2341 Evaluate side-chains 110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.0470 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123565 restraints weight = 7255.554| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.97 r_work: 0.3202 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6304 Z= 0.171 Angle : 0.601 9.037 8603 Z= 0.291 Chirality : 0.040 0.237 1075 Planarity : 0.004 0.064 1044 Dihedral : 7.195 59.299 869 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.64 % Allowed : 27.15 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.31), residues: 788 helix: 1.13 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.32 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.004 0.001 HIS A 327 PHE 0.018 0.001 PHE B 459 TYR 0.013 0.001 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.688 Fit side-chains REVERT: A 104 LYS cc_start: 0.8243 (mptm) cc_final: 0.7816 (mptt) REVERT: A 280 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 359 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.6913 (t80) REVERT: A 394 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.8408 (t-100) REVERT: A 448 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6236 (t80) REVERT: B 51 MET cc_start: 0.9095 (mmt) cc_final: 0.8592 (mmt) REVERT: B 104 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7874 (mptt) REVERT: B 335 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7062 (ptt180) REVERT: B 336 LYS cc_start: 0.8515 (tttp) cc_final: 0.8229 (tttm) REVERT: B 359 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.6998 (t80) REVERT: B 394 TRP cc_start: 0.8943 (OUTLIER) cc_final: 0.8405 (t-100) REVERT: B 448 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.5860 (t80) REVERT: B 451 MET cc_start: 0.6968 (tmm) cc_final: 0.6702 (tmm) outliers start: 44 outliers final: 30 residues processed: 116 average time/residue: 0.1559 time to fit residues: 24.7419 Evaluate side-chains 117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 78 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123894 restraints weight = 7333.408| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.96 r_work: 0.3158 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6304 Z= 0.232 Angle : 0.625 8.992 8603 Z= 0.304 Chirality : 0.041 0.252 1075 Planarity : 0.004 0.062 1044 Dihedral : 7.003 59.278 863 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.64 % Allowed : 26.70 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 788 helix: 1.05 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.31 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.018 0.001 PHE B 459 TYR 0.014 0.002 TYR A 359 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.510 Fit side-chains REVERT: A 104 LYS cc_start: 0.8239 (mptm) cc_final: 0.7835 (mptt) REVERT: A 280 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 394 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.8391 (t-100) REVERT: A 448 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6218 (t80) REVERT: B 51 MET cc_start: 0.9092 (mmt) cc_final: 0.8567 (mmt) REVERT: B 104 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7840 (mptt) REVERT: B 284 ASN cc_start: 0.8404 (t0) cc_final: 0.8061 (t0) REVERT: B 335 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7892 (ptp-170) REVERT: B 336 LYS cc_start: 0.8532 (tttp) cc_final: 0.8256 (tttm) REVERT: B 394 TRP cc_start: 0.8963 (OUTLIER) cc_final: 0.8490 (t-100) REVERT: B 448 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.5831 (t80) REVERT: B 451 MET cc_start: 0.6983 (tmm) cc_final: 0.6708 (tmm) outliers start: 44 outliers final: 34 residues processed: 116 average time/residue: 0.1575 time to fit residues: 24.9374 Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 63 optimal weight: 0.0470 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 0.0270 overall best weight: 0.1948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.156600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124245 restraints weight = 7343.313| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.00 r_work: 0.3225 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6304 Z= 0.149 Angle : 0.592 8.882 8603 Z= 0.282 Chirality : 0.040 0.261 1075 Planarity : 0.004 0.060 1044 Dihedral : 6.826 59.154 863 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.03 % Allowed : 26.85 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.31), residues: 788 helix: 1.25 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.28 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 324 HIS 0.003 0.000 HIS A 166 PHE 0.013 0.001 PHE B 459 TYR 0.013 0.001 TYR A 313 ARG 0.002 0.000 ARG A 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.625 Fit side-chains REVERT: A 104 LYS cc_start: 0.8221 (mptm) cc_final: 0.7823 (mptt) REVERT: A 359 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 394 TRP cc_start: 0.8935 (OUTLIER) cc_final: 0.8367 (t-100) REVERT: A 448 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6332 (t80) REVERT: B 51 MET cc_start: 0.9049 (mmt) cc_final: 0.8561 (mmt) REVERT: B 104 LYS cc_start: 0.8148 (mptm) cc_final: 0.7835 (mppt) REVERT: B 284 ASN cc_start: 0.8248 (t0) cc_final: 0.7978 (t0) REVERT: B 359 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.6963 (t80) REVERT: B 394 TRP cc_start: 0.8938 (OUTLIER) cc_final: 0.8409 (t-100) REVERT: B 448 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.5877 (t80) REVERT: B 451 MET cc_start: 0.6980 (tmm) cc_final: 0.6718 (tmm) outliers start: 40 outliers final: 30 residues processed: 115 average time/residue: 0.1580 time to fit residues: 25.0264 Evaluate side-chains 118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121149 restraints weight = 7437.959| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.01 r_work: 0.3170 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6304 Z= 0.214 Angle : 0.614 8.877 8603 Z= 0.298 Chirality : 0.041 0.258 1075 Planarity : 0.004 0.060 1044 Dihedral : 6.912 59.419 863 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.43 % Allowed : 27.90 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 788 helix: 1.17 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.27 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.015 0.001 PHE B 459 TYR 0.013 0.002 TYR A 359 ARG 0.001 0.000 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3214.19 seconds wall clock time: 57 minutes 44.21 seconds (3464.21 seconds total)